Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations.     

Molecular characterization,expression profile and association analysis with fat deposition traits of the porcine APOM gene

Apolipoprotein M (APOM), a novel apolipoprotein presented mostly in high-density lipoprotein (HDL) in plasma, is involved in lipid and lipoprotein metabolism. Through comparative mapping, we have mapped this gene to SSC7 p1.1 in which many QTLs affecting fat deposition traits have been reported. As a candidate gene for fat deposition traits, in this study, we obtained the 742-bp mRNA sequence of porcine APOM including the full coding region and encoding a protein of 188 amino acids. The sequence was deposited into the GenBank under the accession no. DQ329240. Semi-quantitative RT-PCR results showed that the porcine APOM gene is expressed predominantly in liver and kidney tissue. The genomic sequence of this gene which contains six exons and five introns, is 3,621 bp in length (DQ272488). Bioinformatic analysis of the 5′ regulatory region has revealed that classical TATA-box element and species conserved Hepatocyte nuclear factor-1a (HNF-1α) biding site were represented in this region. A G2289C single nucleotide polymorphism (SNP) in the intron 2 of porcine APOM gene detected as an Eco130I PCR–restriction fragment length polymorphism (PCR–RFLP) showed allele frequency differences among three purebreds. Association of the genotypes with fat deposition traits showed that different genotypes of porcine APOM gene were significantly associated with leaf fat weight (P < 0.05), backfat thickness at shoulder (P < 0.05), backfat thickness at thorax-waist (P < 0.05), backfat thickness at buttock (P < 0.01) and average backfat thickness over shoulder, thorax-waist and buttock (P < 0.01).     

Microarray analysis of high-glucose diet-induced changes in mRNA expression in jejunums of C57BL/6J mice reveals impairment in digestion,absorption

Long term intake of high-glucose diet (HGD) may induce many diseases such as dyslipidemia, fatty liver and diabetes disease. Most of the research for molecular mechanisms of the association between HGD and the above diseases focus on the metabolism of glucose and lipid. However, there are few studies on molecular mechanism of the effect of HGD on digestion and absorption. We used HGD (containing 20% glucose) to feed C57BL/6J mice for 4 weeks, detected the expressions of 13,098 genes in jejunums of C57BL/6J mice with DNA microarray. Microarray analysis showed the expression of genes related to digestive enzyme, gastrointestinal peptide and nutrient transporters were significantly changed, which indicated that HGD induced the suppression of digestive enzyme gene expression, attenuation of alimentary tract movement and nutrient transportation. In one word, the microarray analysis suggested that HGD impaired the function of digestion and absorption in jejunum of C57BL/6J mice. We validated our microarray findings by conducting real-time RT-PCR assays on selected genes and detecting the activities of disaccharidases such as lactase, maltase and sucrase in jejunum of C57BL/6J mice.     

Identification of three novel SNPs and association with carcass traits in porcine <Emphasis Type="Italic">TNNI1</Emphasis> and <Emphasis Type="Italic">TNNI2</Emphasis>

In this study, two novel SNPs (EU743939:g.5174T>C in intron 4 and EU743939:g.8350C>A in intron 7) in TNNI1 and one SNP (EU696779:g.1167C>T in intron 3) in TNNI2 were identified by PCR–RFLP (PCR restriction fragment length polymorphism) using XbaI, MspI and SmaI restriction enzyme, respectively. The allele frequencies of three novel SNPs were determined in the genetically diverse pig breeds including ten Chinese indigenous pigs and three Western commercial pig breeds. Association analysis of the SNPs with the carcass traits were conducted in a Large White × Meishan F₂ pig population. The linkage of two SNPs (g.5174T>C and g.8350C>A) in TNNI1 gene had significant effect on fat percentage. Besides these, the g.5174T>C polymorphism was also significantly associated with skin percentage (P < 0.05), shoulder fat thickness (P < 0.05) and backfat thickness between sixth and seventh ribs (P < 0.05). The significant effects of g.1167C>T polymorphism in TNNI2 gene on fat percentage (P < 0.01), lean meat percentage (P < 0.05), lion eye area (P < 0.05), thorax–waist backfat thickness (P < 0.01) and average backfat thickness (P < 0.05) were also found.     

A single-nucleotide polymorphism of the TNFAIP3 gene is associated with systemic lupus erythematosus in Chinese Han population

Systemic lupus erythematosus (SLE) is a complex systemic disease influenced by genetic and environmental factors. The exact pathogenesis of SLE is still unknown. Recently, several genome-wide association studies (GWA) in European population have found many novel susceptibility genes for SLE including TNFAIP3. In order to examine whether TNFAIP3 is associated with SLE in Chinese Han population, we genotyped one of its non-synonymous mutation SNP rs2230926, showing significant association evidence with SLE in European population, with 1,420 cases and 4,461 controls of Chinese Han by using Sequenom MassArray system. Highly significant association between SNP rs2230926 and SLE of Chinese Han was detected [OR = 1.65, 95% confidence interval (CI): 1.392–1.986, P = 2.03 × 10⁻⁸]. Interestingly, rs2230926 of TNFAIP3 was also associated with arthritis, ANA and some other subphenotypes of the disease. Our findings suggest that SNP rs2230926 in the TNFAIP3 might be a common genetic factor for SLE within different populations in terms of Chinese Han and European population.     

Using K-minimum increment of diversity to predict secretory proteins of malaria parasite based on groupings of amino acids

Due to the complexity of Plasmodium falciparumis genome, predicting secretory proteins of P. falciparum is more difficult than other species. In this study, based on the measure of diversity definition, a new K-nearest neighbor method, K-minimum increment of diversity (K-MID), is introduced to predict secretory proteins. The prediction performance of the K-MID by using amino acids composition as the only input vector achieves 88.89% accuracy with 0.78 Mathew’s correlation coefficient (MCC). Further, the several reduced amino acids alphabets are applied to predict secretory proteins and the results show that the prediction results are improved to 90.67% accuracy with 0.83 MCC by using the 169 dipeptide compositions of the reduced amino acids alphabets obtained from Protein Blocks method.     

千岛湖姥山马尾松种群结构和分布格局研究

为研究千岛湖马尾松(Pinus massoniana)种群动态变化,在姥山岛上设置面积为5.76 hm2的固定样地,进行群落学调查。根据野外调查的数据,对马尾松种群的结构和分布格局进行分析。结果表明:马尾松种群1、2级个体数极少,仅占样地中马尾松个体数的0.06%和1.01%,幼苗、幼树储备严重不足,5级个体的比例最高,达到28.28%,马尾松种群径级结构为纺锤型;马尾松种群的存活曲线为凸型。这些均表明马尾松种群的年龄结构趋向衰退型。但马尾松种群中树个体很多,在较长的时期内马尾松还不会退出群落。马尾松种群静态生命表也可看出中一些小型径级的死亡率为负值,也说明马尾松种群幼苗严重缺乏,种群呈衰退趋势。马尾松种群各径级和总体的分布格局均呈聚集分布,从小树→中树→大树聚集指数逐渐减小,种群呈扩散趋势。     

A novel basic fibroblast growth factor delivery system fabricated with heparin-incorporated fibrin–fibronectin matrices for repairing rat sciatic nerve disruptions

Autologous nerve grafts are widely used in bridging critical gaps of peripheral nerves, but they remain associated with high morbidity of the donor site and lack of full recovery. As an alternative, we have focused on chitosan nerve conduits filled with a heparin-incorporated fibrin–fibronectin matrix serving as delivery systems for basic fibroblast growth factor (bFGF). The artificial nerve conduits were used for repairing sciatic nerve defects of 10 mm in adult rats. Three months post-operation, the conduction velocity recovery index (CVRI) and the muscle restoration rate (MRR) in animals of the experimental group were 32 ± 4.1 and 77.4 ± 7.9%, respectively, which were significantly higher than those of the PBS control group (17.8 ± 1.9 and 66.7 ± 6.5%), and similar to those of the autograft group (38.4 ± 3.9 and 81.3 ± 7.8%). These results were also consistent with the densities of regenerated axons in the three groups, which were demonstrated by histomorphological analysis.     

Robust stability analysis of delayed Takagi-Sugeno fuzzy Hopfield neural networks with discontinuous activation functions

In this paper, the global robust stability problem of delayed Takagi–Sugeno fuzzy Hopfield neural networks with discontinuous activation functions (TSFHNNs) is considered. Based on Lyapunov stability theory and M-matrices theory, we derive a stability criterion to guarantee the global robust stability of TSFHNNs. Compared with the existing literature, we remove the assumptions on the neuron activations such as Lipschitz conditions, bounded, monotonic increasing property or the assumption that the right-limit value is bigger than the left one at the discontinuous point. Finally, two numerical examples are given to show the effectiveness of the proposed stability results.